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- PDB-6pac: E. coli L-asparaginase II in complex with L-Asp at pH 5.6 -

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Basic information

Entry
Database: PDB / ID: 6pac
TitleE. coli L-asparaginase II in complex with L-Asp at pH 5.6
ComponentsL-asparaginase 2
KeywordsHYDROLASE / inactive mutant / hydrolysis of L-asparagine
Function / homology
Function and homology information


L-asparagine catabolic process / asparaginase / asparaginase activity / outer membrane-bounded periplasmic space / protein homotetramerization / periplasmic space / protein-containing complex / identical protein binding
Similarity search - Function
L-asparaginase, N-terminal domain / Rossmann fold - #40 / L-asparaginase, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. ...L-asparaginase, N-terminal domain / Rossmann fold - #40 / L-asparaginase, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. / Asparaginase / Asparaginase/glutaminase-like / L-asparaginase, N-terminal / Asparaginase/glutaminase-like superfamily / L-asparaginase, N-terminal domain superfamily / Asparaginase, N-terminal / Asparaginase / glutaminase domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / IMIDAZOLE / L-asparaginase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsLubkowski, J. / Wlodawer, A.
CitationJournal: Protein Sci. / Year: 2019
Title: Geometric considerations support the double-displacement catalytic mechanism of l-asparaginase.
Authors: Lubkowski, J. / Wlodawer, A.
History
DepositionJun 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-asparaginase 2
B: L-asparaginase 2
C: L-asparaginase 2
D: L-asparaginase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,47810
Polymers142,8084
Non-polymers6716
Water30,4451690
1
A: L-asparaginase 2
B: L-asparaginase 2
hetero molecules

A: L-asparaginase 2
B: L-asparaginase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,3408
Polymers142,8084
Non-polymers5324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15790 Å2
ΔGint-49 kcal/mol
Surface area42360 Å2
MethodPISA
2
C: L-asparaginase 2
D: L-asparaginase 2
hetero molecules

C: L-asparaginase 2
D: L-asparaginase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,61712
Polymers142,8084
Non-polymers8098
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area16760 Å2
ΔGint-34 kcal/mol
Surface area40790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.178, 62.395, 140.665
Angle α, β, γ (deg.)90.000, 117.550, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-702-

HOH

21B-658-

HOH

31C-779-

HOH

41D-753-

HOH

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Components

#1: Protein
L-asparaginase 2 / L-asparaginase II / L-ASNase II / L-asparagine amidohydrolase II


Mass: 35701.965 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Expressed variant contains 8 additional N-terminal residues MDHHHHHH (affinity tag)
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ansB, b2957, JW2924 / Plasmid: pET22b(+)
Details (production host): contains secretion sequence pelB leader
Cell (production host): bacteria / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): JC2 strain lacking in ansA / References: UniProt: P00805, asparaginase
#2: Chemical
ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1690 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Crystals were grown in 0.17 M NH4-citrate, pH 5.6, 17-18% PEG3350, then soaked for 1 min in solution with 5 mM L-Asp

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jun 24, 2018 / Details: Multilayer X-ray mirrors VariMax HF
RadiationMonochromator: Multilayer X-ray mirrors VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 135099 / % possible obs: 88 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.019 / Rpim(I) all: 0.013 / Rrim(I) all: 0.024 / Χ2: 0.712 / Net I/σ(I): 21 / Num. measured all: 337531
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.631.40.26941890.710.2430.3650.71354.9
1.63-1.661.50.26547940.6230.2320.3540.71563.2
1.66-1.691.60.23955940.8680.20.3140.69473
1.69-1.721.80.21364730.9020.1670.2730.69284.7
1.72-1.7620.17969590.9330.1360.2260.66991.2
1.76-1.82.40.16872290.9510.1160.2050.71394.4
1.8-1.852.50.12671500.9710.0870.1550.68793.6
1.85-1.92.50.10670990.980.0740.130.68692.7
1.9-1.952.60.07970410.9870.0550.0970.71591.7
1.95-2.022.70.06469620.9910.0440.0790.74191.6
2.02-2.092.70.05669380.990.0380.0680.83990.3
2.09-2.172.70.04367650.9950.0290.0530.85188.6
2.17-2.272.70.03767010.9950.0250.0450.90386.8
2.27-2.392.60.03165980.9950.0210.0370.86886.3
2.39-2.542.60.02767320.9940.0190.0330.84487.9
2.54-2.742.50.02171740.9970.0150.0260.77392.7
2.74-3.012.70.01674130.9980.0110.020.71196.5
3.01-3.452.90.01276970.9990.0080.0140.59699.4
3.45-4.342.90.00977380.9990.0060.0110.52899.8
4.34-403.30.00978530.9990.0060.0110.49699

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→40 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.1582 / WRfactor Rwork: 0.1205 / FOM work R set: 0.8932 / SU B: 1.588 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0807 / SU Rfree: 0.0856 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1719 3432 2.5 %RANDOM
Rwork0.1308 ---
obs0.1318 131536 88.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 104.77 Å2 / Biso mean: 20.616 Å2 / Biso min: 5.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.02 Å2
2---0.11 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9670 0 46 1725 11441
Biso mean--19.66 31.03 -
Num. residues----1292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0199946
X-RAY DIFFRACTIONr_bond_other_d0.0020.029166
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.95613570
X-RAY DIFFRACTIONr_angle_other_deg1.075321335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20951314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.36225.971417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.147151614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4851532
X-RAY DIFFRACTIONr_chiral_restr0.1250.21621
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111264
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021801
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 163 -
Rwork0.279 6262 -
all-6425 -
obs--57.13 %

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